Richard,
I put the SE 6-spd on mine back in late March, 2008. It is all good now, but I was pretty upset with the cheap little plate and gasket HD used to cover the old speed sensor location on the case (as in when these cases were used for the 5-spd). HD may have fixed this, but if not, Jims has a much better fix (see #8102 on the attached). All up cost me about $3k for the tranny, side cover kit, gaskets, fluids, etc. I did get a 10% discount from the HD Dealership just cause I asked for it.
Shifting down to 6th is good. If you run some highway speeds for any length of time, it is more comfortable. Probably worth it, but that is a judgement call. Save your old tranny, unless you get the gear set and have that installed in the current case in which case there is no old tranny, just the old gear set (save that!).
As I said above, if I was doing it again, I would be hard pressed on what to choose - Baker DD6 or SE 6-spd. When I did mine, I looked into the tools I would need to do it and it was too expensive to buy all that AND the Baker gear set. I think at this point I would be able to borrow the tools or buy them on the cheap, so the Baker option is more realistic. But the Baker DD6 gear set is about the same price as the complete SE 6-spd. So ...
TQ